RNA Modification


Naturally occurring ribonucleic acids (RNAs) contain over 150 chemically altered nucleosides formed by enzymatic modification of the primary RNA transcript during the complex tRNA maturation process. This post‐transcriptional RNA modification is a universally conserved and highly complex metabolic process in the living cell. Cellular RNAs are modified by pure protein stand‐alone enzymes, as well as by s(sno)RNP complexes containing guide s(sno)RNAs. Modified nucleotides present in RNA play an important role in stabilisation of 2D and 3D structures of these molecules, as well as in the fine‐tuning of numerous interactions between RNAs itself and with RNA‐binding protein partners. Modification also protects RNAs against nucleolytic degradation and improves their performance in different interactions in which various RNAs are involved. For example, modifications present in the tRNA anticodon loop are crucially important for correct mRNA decoding during the protein synthesis on the ribosome. Recent progress in the field points out the regulatory character of RNA modification. This emerging concept of ‘RNA‐epigenetics’ supplies the additional level to the regulation of gene expression. This regulation (and deregulation) of RNA‐modification machineries is a basis for some important human pathologies.

Key Concepts

  • Cellular RNAs are post‐transcriptionally modified in all life kingdoms
  • RNA modification alters physico‐chemical properties of nucleotides, including their conformation, polarity, hydrophobicity, chemical reactivity and base‐pairing interactions
  • RNA modification is performed by highly specific and regulated enzymatic mechanisms involving pure protein enzymes and catalytic RNA–protein complexes (RNPs)
  • RNA modification is important for regulation of gene expression
  • Transcription‐wide RNA modification is dynamic and regulated cellular process
  • Deregulation of RNA modification may lead to important human pathologies

Keywords: modified nucleotides; methylation; thiolation; pseudouridine; anticodon; mRNA decoding

Figure 1. Types of chemical alterations and their location within the purine and pyrimidine derivatives in all kinds of RNAs (tRNA, rRNA, mRNA, snRNA, etc.) from various organisms. The groups that differentiate from the canonical A, G, C or U are in red. Base positions are numbered in blue (conventional numbering for purine and pyrimidine rings). In naturally occurring RNAs, various combinations of different modifications exist, thus extending the total number of the modified nucleosides present in RNAs over 140. Modified A and inosine (I) nucleotides (a), G nucleotides (b), 2′‐O‐modifications (c), modified C residues (d), modified U and Ψ derivatives (e) and 7‐deaza and queuosine (Q) derivatives (f). Except for 7‐deazaguanosine and queuosine derivatives, the purine and pyrimidine ring (in black) are those initially encoded in RNA during transcription. For more details about the chemistry and occurrence of modified nucleosides in RNA, see (Sprinzl et al., ) or (Cantara et al., ).
Figure 2. Phylogenetic distribution of modified nucleosides in RNA originating from the three domains of life. Abbreviations of modified nucleosides are as in Figure. Data presented in this figure may be in contradiction with other sources owing to: (1) limited information available on the RNA sequence of many Archaea RNAs, (2) discrepancies between direct tRNA sequencing data and global nucleoside composition analysis by HPLC‐MS and (3) errors, misinterpretation or misidentification of modified residues in tRNA molecules. Compilation was performed using RNA‐modification database and MODOMICS database (Cantara et al., ; Czerwoniec et al., ).
Figure 3. (a) Wire structure of C/D and H/ACA‐box snoRNAs. The conserved sequences (boxes C/D and C′/D′ in C/D snoRNA and H and ACA boxes in H/ACA snoRNA) are indicated. (b) Schematic representation of the assembled C/D sRNPs structure obtained by NMR, adapted from Lapinaite et al., (). sno(s)RNA guide is shown in orange, the substrate RNA in red, and positions of conserved proteins of C/D particle (Nop5, fibrillarin (Fib) and L7ae) are defined on the basis of high‐resolution structure. Conserved sequences of Boxes D′ in sRNA are indicated. (c) Schematic representation of H/ACA s(sno)RNP particles, the expected locations of snoRNP proteins are indicated. Adapted with permission from Wang, C. and Meier, U.T. (2004). © European Molecular Biology Organization.
Figure 4. Cellular localisation of RNA:modification enzymes and coordination between RNA (tRNA) maturation and modification. The scheme describes in detail the maturation of eukaryotic tRNAs, but may also be generalised to other RNA molecules. Transcription of RNA genes happens in the nucleus, and after short initial folding, RNA‐modification enzymes modify these nascent RNA transcripts (early nuclear modifications). Maturation proceeds by 5′‐ and 3′‐trimming and concomitant action of other components of RNA‐modification machinery (late nuclear modifications). Some RNAs transit through the nucleolus and are modified there by snoRNA RNPs (C/D and H/ACA). tRNA introns are spliced at the level of nuclear pore, and almost mature tRNAs are released to the cytoplasm, where some additional (late cytoplasmic) modifications take place. Eukaryotic mitochondrial tRNAs are mostly produced inside the mitochondria and modified there by imported RNA:modification enzymes. In some instances tRNAs are further imported from the cytoplasm to the organelles (mitochondria and chloroplasts).
Figure 5. Major concepts of RNA (tRNA) recognition by RNA:modification enzymes. (a) Identity elements (specific nucleotides indicated by orange dots) insure recognition of unique (or few RNA substrates). (b) Recognition of global 3D architecture of the RNA molecule, 3D tRNA core is indicated in red and overall 3D structure is outlined in dark blue. (c) Recognition of local structural domain which may be present in different RNA molecules. Anticodon stem‐loop and Tψ‐stem‐loop are highlighted in green and orange, respectively. (d) Concept of separate RNA guide to govern RNA‐substrate recognition. Target RNA does not contain any identity element and the enzyme recognises the duplex formed by target RNA and RNA guide (example of s(sno)‐RNA‐guided 2′‐O‐methylathion). In this case the guide contains the recognised sequence.
Figure 6. Modification alters physico‐chemical and base‐pairing properties of nucleotides. Examples of modified residues derived from A (a), G (b), C (c) and U (d). Additional chemical groups are shown in red and parental nucleotide in black. Modified nucleotide m7G (b) specifically reacts with NaBH4, m5C (C) is not deaminated by Na2SO3, compared to unmodified C. Pseudouridine (d) reacts with soluble carbodiimides such as CMCT, s2U with organomercuric substances and 2′‐O‐Me groups bring resistance to alkaline cleavage. Other modifications affect hydrophobicity, conformation (Ψ and D (d)) and base‐pairing properties.
Figure 7. Known functions of RNA modification. The presence of modified residues in RNA: affects the overall thermostability of RNA molecules (a), adapted with permission from Cabello‐Villegas, J. and Nikonowicz, E.P. (). © Oxford University Press, or affects their resistance to endonuclease cleavages (case of 2′‐O‐Me) (b) and modulates the antibiotic resistance of bacteria by appropriate rRNA modification (c), adapted from Wilson, D.N. (). © Nature Publishing Group. Modified residues also modulate the tRNA recognition by TLR7 receptors and thus modulate immune response (d), adapted from Hori, H. () and affect recognition of tRNAs and other RNAs by specific proteins (e), adapted from Suzuki, T. and Miyauchi, K. (). © Elsevier. At the level of translation, modified nucleotides in tRNA and in mRNA affect codon–anticodon recognition and thus mRNA decoding by the ribosome (f) (PDB structure 1XMO, tRNALys(UUU)), modulate frameshifting efficiency (g). Finally, widespread modification of mRNAs in eukaryotic cells (m6A and Ψ) is supposed to control gene expression (h) Liu et al. ().


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Further Reading

Grosjean H and Benne R (eds) (1999) The Modification and Editing of RNA. New York, NY: ASM Press.

Grosjean H (ed) (2009) DNA and RNA Modification Enzymes: Structure, Mechanism and Evolution. Austin: Landes Bioscience.

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Motorin, Yuri(May 2015) RNA Modification. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000528.pub3]